openbabel SKILL.md skillA
openbabel from jinzhezenggroup/computational-chemistry-agent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jinzhezenggroup/computational-chemistry-agent-skills/openbabel@v1.1Pins v1.1 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jinzhezenggroup/computational-chemistry-agent-skills
- Path
data-processing/openbabel/SKILL.md- Versions recorded
- 4
- Latest version
- v1.1, committed May 27, 2026
- First version recorded
- Mar 17, 2026
- Size
- 3,399 bytes
- Repository stars
- 156
- License
- LGPL-3.0
A versatile CLI tool for converting molecular file formats, generating 3D atomic coordinates from SMILES, rendering 2D chemical structure images, and preparing or extracting structures for computational workflows. USE WHEN you need to convert between chemical file formats (e.g., xyz, pdb, mol, smi, gjf), generate 3D structures from SMILES using `--gen3d`, render molecule images (PNG/SVG), or extract geometries from simulation logs to build new inputs.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# Open Babel This skill provides practical Open Babel command patterns for common chemistry data tasks. ## Quick Start Check installation through uvx: ```bash uvx --from openbabel obabel -V ``` Typical conversion syntax: ```bash uvx --from openbabel obabel input.ext -i<input_format> -o<output_format> -O output.ext ``` ## Core Tasks ### 1) File format conversion Convert XYZ to PDB: ```bash uvx --from openbabel obabel C.xyz -ixyz -opdb -O C.pdb ``` Open Babel supports a large set of chemistry formats (e.g., xyz, mol, mol2, pdb, smi, Gaussian gjf/log/fchk, etc.). ### 2) Build structures from SMILES Generate methane (3D coordinates required): ```bash uvx --from openbabel obabel -:C --gen3d -omol -O C.mol ``` Generate a single carbon atom: ```bash uvx --from openbabel obabel -:[C] --gen3d -omol -O C.mol ``` Generate methyl radical: ```bash uvx --from openbabel obabel -:[CH3] --gen3d -omol -O CH3.mol ``` > Important: quote SMILES when they contain brackets or special characters. Equivalent explicit form: ```bash uvx --from openbabel obabel -:"[C]([H])([H])[H]" --gen3d -omol -O CH3.mol ``` ### 3) Export SMILES from one or more structure files ```bash …
Read the whole file at its exact version.
How to install
mdr add jinzhezenggroup/computational-chemistry-agent-skills/openbabel@sha256:38f52fda361c8b67The line at the top of this page pins the label v1.1, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_3dfb7r5nmojglbqk)
2 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 4 versions of this file, between Mar 17, 2026 and May 27, 2026, about one every 24 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| v1.1 latest | 2026-05-27 | 7f53de1 | 3,399 B | A | view · diff |
| v1.1 | 2026-03-23 | 622da72 | 3,501 B | A | view · diff |
| v1.1 | 2026-03-21 | 0fbe96d | 3,474 B | A | view · diff |
| v1.1 | 2026-03-17 | d0e4cd7 | 3,202 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (3399 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
jinzhezenggroup/computational-chemistry-agent-skills · 156 stars · license LGPL-3.0 · pushed 2026-11-02 · branch master
API
GET https://markdownregistry.com/api/v1/artifacts/art_3dfb7r5nmojglbqk GET https://markdownregistry.com/api/v1/resolve?ref=jinzhezenggroup/computational-chemistry-agent-skills/openbabel GET https://markdownregistry.com/api/v1/blob/38f52fda361c8b67495e40a665d228fe6dc3230d9661556ed1c62bb40f985d89
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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